It's not a problem of passing such a big array but rather a problem with 
processing it. You didn't show your code but it probably looks like that:

void native_function(JNIEnv *env, jobject thiz, jobjectArray jarray) {
   ...
   for (int i = 0; i < env->GetArrayLength(jarray); i++) {
      jstring jstr = env->GetObjectArrayElement(jarray, i); // you creating 
local ref here
      // do somthing with string
   }
   ...
}

such code will overflow local ref table, causing error you've cited. You 
should always delete local ref at the end of body loop to avoid this.

--
Bart

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